Haplotype and linkage disequilibrium analysis has contributed to studies on recombination and human gene mapping. This project develops an algorithm to obtain maximum likelihood estimates of haplotype frequencies from phenotypic data, and it develops a set of hypotheses that can be statistically tested in order to demonstrate pairwise and higher order linkage disequilibrium. A computer program was written to implement the methods. The utility of the methods and computer program is verified using Monte Carlo simulations. This work will be applicable to the many short tandem repeat DNA polymorphisms that our lab is typing for linkage analyses.